Dindel protocols

Dindel computational protocol

Dindel specifications


Unique identifier OMICS_00096
Name Dindel
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Mapped Illumina read data
Input format BAM
Output data Variant calls
Output format VCF
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Cornelis Albers <>

Publication for Dindel

Dindel IN pipelines

PMCID: 5069154
PMID: 27642863
DOI: 10.1038/nchembio.2176

[…] strain, a best call was made based on the aligned reads for each strain, and positions where all strains supported a variant were discarded. small insertions and deletions (indels) were called using dindel34. candidate indels found in one strain were explicitly tested for in all strains; indels with at least 70% of reads in the region supporting the indel and at positions with an average […]

PMCID: 5389031
PMID: 25633131
DOI: 10.1038/srep08132

[…] pcc 6301 and synechococcus pcc 7942 genome data obtained from genbank (nc_006576 and nc_007604, respectively) using novoalign. samtools was used to identify snps between the two strains. dindel was used to identify indels. pindel and custom analyses were used to identify structural rearrangements. 454 genome sequencing was also performed in parallel (mogene lc, st. louis, mo) […]

PMCID: 3991715
PMID: 24748104
DOI: 10.1371/journal.pone.0095783

[…] procedure. this resulted in 5,236,586 biallelic snps with a “pass” tag in the quality field, and has reference snp number (dbsnp137). insertion/deletion polymorphism (indel) was called by using dindel (version 1.01) [28] using the realigned bam files as input. out of 1,194,452 calls, 792,607 biallelic indels that passed quality check and documented in dbsnp137 were also used. snp and indel […]

PMCID: 4306819
PMID: 25497598
DOI: 10.1093/brain/awu348

[…] 1 and 2. in-house bioinformatic analysis included alignment to ucsc hg19, using burrows-wheeler aligner; duplicate removal (picard v1.85) and variant detection (varscan v2.2) (koboldt et al., 2009), dindel v1.01 (albers et al., 2011). further analysis was performed on variants with a minor allele frequency <0.01 in several databases: dbsnp137, 1000 genomes (april 2012 data release), […]

PMCID: 3618354
PMID: 23550133
DOI: 10.1534/g3.113.005660

[…] elements were identified using repeatmasker (version open-3.3.0) (smit et al. 1996-2010). structural variation was detected using breakdancer (chen et al. 2009), crest (wang et al. 2011), and dindel (albers et al. 2011). details are provided in file s1., details of molecular techniques are given in file s1 in the supplementary information. avc1 was amplified from h99, cloned […]

Dindel institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK

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